As a method for detecting excess, deletion, amplification and the like abnormal copy numbers of genomic DNA using chromosomes as the object, there is a genomic CGH method which has been developed by Joe Gray, Dan Pinkel, O-P Kallioniemi et al. In general, there were various problems in that a chromosomal aberrancy cannot be detected except that it is within a large region covering from 5 to 10 Mb or more, skills are required for the analysis, and the like (J. Inazawa and M. Minaguchi, Rinsho Kensa (Clinical Inspection), 49, 497-502 (2005)).
There is an array CGH method as a tool which can detect a genomic structure aberrancy occurred at a level of from several 10 kb to several Mb, higher than the resolution that can be analyzed by chromosomal analyses (D. Pinkel et al., Nat. Genet., 20, 207-211 (1998) and I. Imoto and J. Inazawa, Saibo Kogaku (Cell Engineering), 23, 355-361 (2004)). The array CGH method uses an array in which fragments of genomic DNA, such as BAC (bacterial artificial chromosomes) clones, YAC (yeast artificial chromosomes) clones, PAC (P1-derived artificial chromosomes) or DNAs or oligonucleotides prepared based on these BAC, YAC, PAC and the like, are arranged on a solid substrate by spotting them on the substrate. In addition, this is a method for detecting relative numbers of copies of genes, by extracting target DNA samples from an abnormal cell to be used as a sample to be tested collected from a patient or the like and a normal cell to be used as a standard sample collected from a healthy person, labeling them with respectively different labels (fluorescent materials or the like), allowing them to simultaneously contact with a probe on the nucleic acid microarray, thereby allowing them to undergo interaction via hybridization, reading off fluorescence signals generated from the interacted target nucleic acids using a scanner or the like, and comparing intensity ratios of the signals of the normal cell- and abnormal cell-derived target nucleic acids.
When a sample and a standard are labeled with respectively different labeling compounds and allowed to hybridize with a nucleic acid microarray in carrying out an analysis which uses the nucleic acid microarray, the difference in data caused by different spots (spotted amount or the like) or the like or by a difference in hybridization, generated between batches of the microarray, hardly occurs. However, since the labeling is different, a difference in labeling efficiency, a difference in the detection system for individual labeling, and the like are apt to exert influence on the result, and it accompanies a complexity of always requiring preparation of the standard for one sample to be tested. In order to exclude the difference in labeling, the problem does not occur when a method is employed in which the standard and sample to be tested are labeled with the same labeling compound and allowed to undergo hybridization separately with two or more nucleic acid arrays, and the evaluation is carried out between them. However, a problem is generated by this method, in which the data fluctuation due to difference in spot once resolved by simultaneously carrying out the hybridization is again generated in carrying out separate labeling. As a method for solving these problems, there is a method in which a difference between arrays is corrected by newly mounting a spot for correction and internal standard use on the microarray, but it cannot correct the difference between separate spots (e.g., JP-A-2004-028695).